2024
NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development
Strayer E, Krishna S, Lee H, Vejnar C, Neuenkirchen N, Gupta A, Beaudoin J, Giraldez A. NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development. Nature Communications 2024, 15: 10898. PMID: 39738051, PMCID: PMC11685710, DOI: 10.1038/s41467-024-55274-y.Peer-Reviewed Original ResearchConceptsMassively parallel reporter assaysCis-regulatory elementsMaternal-to-zygotic transitionGC-rich motifsU-rich motifsTrans-acting proteinsRepressor of translationRibosome affinity purificationRegulatory grammarUpstream ORFsZygotic expressionTranslational switchReporter mRNATranslational controlTranslational regulationNascent peptideAffinity purificationMicroRNA sitesPolysome profilingMRNA translationZebrafish developmentMRNA stabilityExpression of miR-430MiR-430Regulatory functionsUPF1 regulates mRNA stability by sensing poorly translated coding sequences
Musaev D, Abdelmessih M, Vejnar C, Yartseva V, Weiss L, Strayer E, Takacs C, Giraldez A. UPF1 regulates mRNA stability by sensing poorly translated coding sequences. Cell Reports 2024, 43: 114074. PMID: 38625794, PMCID: PMC11259039, DOI: 10.1016/j.celrep.2024.114074.Peer-Reviewed Original ResearchConceptsUpstream open reading framesOpen reading frameRegulate mRNA stabilityNonsense-mediated decayMRNA stabilityReading frameOpen reading frame lengthRegulate mRNA decayAU-rich elementsMicroRNA binding sitesCis-elementsTranslation initiationStop codonMRNA decayCodon optimizationUPF1Gene expressionBinding sitesCodonMRNAConvergent rolesHigher decay ratesMachine-learning analysisUTR
2019
Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
Vejnar CE, Messih M, Takacs C, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee M, Beaudoin JD, Musaev D, Darwich-Codore H, Walther T, Tavazoie S, Cifuentes D, Giraldez A. Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. Genome Research 2019, 29: 1100-1114. PMID: 31227602, PMCID: PMC6633259, DOI: 10.1101/gr.245159.118.Peer-Reviewed Original ResearchConceptsAU-rich elementsMRNA stabilityZygotic transitionRich motifGenome-wide analysisRNA-protein interactionsGenome activationParallel reporterCombinatorial regulationMaternal transcriptsMiR-430Destabilizing motifsRegulatory motifsWide analysisMRNA deadenylationPosttranscriptional regulationRegulatory sequencesMost transcriptsMultiple decay pathwaysUTR sequencesSequence elementsGene expressionTarget sequenceDecay pathwaysMotif
2016
Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition
Bazzini AA, del Viso F, Moreno‐Mateos M, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ. Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition. The EMBO Journal 2016, 35: 2087-2103. PMID: 27436874, PMCID: PMC5048347, DOI: 10.15252/embj.201694699.Peer-Reviewed Original ResearchConceptsZygotic transitionMRNA stabilityTranslation efficiencyMRNA clearanceMaternal mRNAsCodon identityCodon compositionGene expressionMaternal mRNA clearanceRegulated mRNA decayPost-transcriptional mechanismsAmino acid sequenceTranscript decayMRNA decayPolyadenylation statusAmino acid compositionCodon tripletsGenetic codeSynonymous codonsAcid sequenceCellular transitionsRegulatory informationNew transcriptionDevelopmental progressionMRNA
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